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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

PCDHGA3 Gene

protein-coding   GIFtS: 41
GCID: GC05P141297

Protocadherin Gamma Subfamily A, 3

  See related disease
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
About This Section

Aliases
Protocadherin Gamma Subfamily A, 31 2
PCDH-GAMMA-A32
Protocadherin Gamma-A32
PCDH-gamma-A33

External Ids:    HGNC: 87011   Entrez Gene: 561122   Ensembl: ENSG000002542457   OMIM: 6062905   UniProtKB: Q9Y5H03   

Export aliases for PCDHGA3 gene to outside databases

Previous GC identifers: GC05P140540 GC05P141302 GC05P140702 GC05P140747 GC05P140781 GC05P140699 GC05P140810 GC05P141035 GC05P135868 GC05P141101 GC05P141139 GC05P141179 GC05P141210 GC05P141249


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

Entrez Gene summary for PCDHGA3 Gene:
This gene is a member of the protocadherin gamma gene cluster, one of three related clusters tandemly linked on
chromosome five. These gene clusters have an immunoglobulin-like organization, suggesting that a novel mechanism
may be involved in their regulation and expression. The gamma gene cluster includes 22 genes divided into 3
subfamilies. Subfamily A contains 12 genes, subfamily B contains 7 genes and 2 pseudogenes, and the more
distantly related subfamily C contains 3 genes. The tandem array of 22 large, variable region exons are followed
by a constant region, containing 3 exons shared by all genes in the cluster. Each variable region exon encodes
the extracellular region, which includes 6 cadherin ectodomains and a transmembrane region. The constant region
exons encode the common cytoplasmic region. These neural cadherin-like cell adhesion proteins most likely play a
critical role in the establishment and function of specific cell-cell connections in the brain. Alternative
splicing has been described for the gamma cluster genes. (provided by RefSeq, Jul 2008)

GeneCards Summary for PCDHGA3 Gene: 
PCDHGA3 (protocadherin gamma subfamily A, 3) is a protein-coding gene. Diseases associated with PCDHGA3 include neuronitis. GO annotations related to this gene include calcium ion binding. An important paralog of this gene is PCDHAC1.

UniProtKB/Swiss-Prot: PCDG3_HUMAN, Q9Y5H0
Function: Potential calcium-dependent cell-adhesion protein. May be involved in the establishment and maintenance
of specific neuronal connections in the brain




(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the PCDHGA3 gene promoter:
         Max1   AREB6   Sp1   AP-1   ATF-2   c-Jun   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidPCDHGA3 promoter sequence
   Search SABiosciences Chromatin IP Primers for PCDHGA3

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat PCDHGA3


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 5q31   Ensembl cytogenetic band:  5q31.3   HGNC cytogenetic band: 5q31

PCDHGA3 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
PCDHGA3 gene location

GeneLoc information about chromosome 5         GeneLoc Exon Structure

GeneLoc location for GC05P141297:  view genomic region     (about GC identifiers)

Start:
140,723,601 bp from pter      End:
140,892,546 bp from pter
Size:
168,946 bases      Orientation:
plus strand

(According to UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB/Swiss-Prot: PCDG3_HUMAN, Q9Y5H0 (See protein sequence)
Recommended Name: Protocadherin gamma-A3 precursor  
Size: 932 amino acids; 100971 Da
Subcellular location: Cell membrane; Single-pass type I membrane protein (By similarity)
Secondary accessions: Q9Y5D4
Alternative splicing: 2 isoforms:  Q9Y5H0-1   Q9Y5H0-2   

Explore the universe of human proteins at neXtProt for PCDHGA3: NX_Q9Y5H0

Explore proteomics data for PCDHGA3 at MOPED 

Post-translational modifications:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_Q9Y5H0

  • PCDHGA3 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    PCDHGA3 Protein Expression
    REFSEQ proteins (2 alternative transcripts): 
    NP_061739.2  NP_114400.1  

    ENSEMBL proteins: 
     ENSP00000253812  

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    Browse Proteins at Cloud-Clone Corp. 

    Gene Ontology (GO): 3 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005886plasma membrane IEA--
    GO:0016020membrane ----
    GO:0016021integral to membrane IEA--

    PCDHGA3 for ontologies           About GeneDecksing



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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    HGNC Gene Families: 
    PCDHC: Cadherins / Protocadherins : Clustered

    4 InterPro protein domains:
     IPR015919 Cadherin-like
     IPR013164 Cadherin_N
     IPR020894 Cadherin_CS
     IPR002126 Cadherin

    Graphical View of Domain Structure for InterPro Entry Q9Y5H0

    ProtoNet protein and cluster: Q9Y5H0

    1 Blocks protein domain: IPB002126 Cadherin

    UniProtKB/Swiss-Prot: PCDG3_HUMAN, Q9Y5H0
    Similarity: Contains 6 cadherin domains


    PCDHGA3 for domains           About GeneDecksing


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
    About This Section

    Molecular Function:

         UniProtKB/Swiss-Prot Summary: PCDG3_HUMAN, Q9Y5H0
    Function: Potential calcium-dependent cell-adhesion protein. May be involved in the establishment and maintenance
    of specific neuronal connections in the brain

         Gene Ontology (GO): 1 molecular function term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005509calcium ion binding IEA--
         
    PCDHGA3 for ontologies           About GeneDecksing


    Animal Models:
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    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene).
    About This Section




    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for PCDHGA3

    Gene Ontology (GO): 1 biological process term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0007156homophilic cell adhesion IEA--

    PCDHGA3 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for PCDHGA3 (PCDG3)

    1 HMDB Compound for PCDHGA3    About this table
    CompoundSynonyms CAS #PubMed Ids
    CalciumCa (see all 2)7440-70-2--

    Search CenterWatch for drugs/clinical trials and news about PCDHGA3 / PCDG3

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for PCDHGA3 gene (2 alternative transcripts): 
    NM_018916.3  NM_032011.1  

    1 Ensembl transcript including schematic representation, and UCSC links where relevant:
    ENST00000253812(uc003ljm.2)
    miRNA
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    hsa-miR-1226 hsa-miR-448 hsa-miR-4272 hsa-miR-765 hsa-miR-624* hsa-miR-650 hsa-miR-3150a-3p hsa-miR-548a-3p
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    24/737 AceView cDNA sequences (see all 737):

    AF152327 AL536915 BU627870 BQ183224 AI244602 AW002439 BC004321 CA390638 
    AF152518 AB000896 BM694643 AF152517 AF152520 BC027470 AA999664 BU196653 
    BG818666 BQ318895 NM_018915 CA442860 NM_018928 AF152323 CA392030 CR614457 

    GeneLoc Exon Structure


    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    PCDHGA3 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: --
    PCDHGA3 Expression
    About this image


    See PCDHGA3 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for PCDHGA3
        SABiosciences Custom PCR Arrays for PCDHGA3
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    In Situ
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    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
    About This Section

    This gene was present in the common ancestor of chordates.

    Orthologs for PCDHGA3 gene from 3/9 species (see all 9)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Pcdhga31 , 5 protocadherin gamma subfamily A, 31, 5 83.22(n)1
    85.79(a)1
      18 (19.55 cM)5
    937111  NM_033586.21  NP_291064.11 
     376743355 
    lizard
    (Anolis carolinensis)
    Reptilia --
    --
    (see all 10)
    Uncharacterized protein
    (see all 10)
    54(a)
    53(a)
    (see all 10)
    many ↔ many
    many ↔ many
    (see all 10)
    4(76897250-76899667)
    4(76856421-76858829)
    zebrafish
    (Danio rerio)
    Actinopterygii pcdh1g96
    BX119910.156
    (see all 24)
    Uncharacterized protein
    (see all 24)
    47(a)
    46(a)
    (see all 24)
    many ↔ many
    many ↔ many
    (see all 24)
    10(21767295-21770275)
    10(21770733-21773977)


    ENSEMBL Gene Tree for PCDHGA3 (if available)
    TreeFam Gene Tree for PCDHGA3 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for PCDHGA3 gene
    PCDHAC12  PCDHB162  PCDHB22  PCDHAC22  PCDHB72  PCDHB152  PCDHGA102  PCDHGB22  
    PCDHGA122  PCDHGA92  PCDHGA82  PCDHGC32  PCDHGA52  PCDHA82  PCDHB52  PCDHB132  
    PCDHGA42  PCDHGA72  PCDHB42  PCDHB112  PCDHA22  ENSG000002556222  PCDHB142  PCDHB122  
    PCDHB82  PCDHGB12  PCDHGB42  PCDHA52  PCDHGA22  PCDHGA62  PCDHB32  PCDHGA112  
    PCDHB62  PCDHGC42  PCDHGC52  PCDHGA12  PCDHB102  PCDHB12  PCDHGB72  
    18/73 SIMAP similar genes for PCDHGA3 using alignment to 5 protein entries:     PCDG3_HUMAN (see all proteins) (see all similar genes):
    PCDHGA2    PCDHGA4    PCDHGA7    PCDHGA8    PCDHGA1    PCDHGA10
    PCDHGA5    PCDHGA11    PCDHGA12    PCDHGA9    PCDHGA6    PCDHGC3
    ME3    PCDHGB2    PCDHGB7    PCDHGB4    PCDHGB5    PCDHGB1

    PCDHGA3 for paralogs           About GeneDecksing



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    3 SNPs in PCDHGA3 are shown    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 5 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    VAR_0591904
    ----see VAR_0591902 A V mis40--------
    VAR_0555894
    ----see VAR_0555892 I L mis40--------
    VAR_0555884
    ----see VAR_0555882 P S mis40--------

    HapMap Linkage Disequilibrium report for PCDHGA3 (140723601 - 140892546 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 10/15 variations for PCDHGA3 (see all 15):    About this table     
    Variant IDTypeSubtypePubMed ID
    esv2730847CNV Deletion23290073
    esv267823CNV Insertion20981092
    nsv823280CNV Loss20364138
    nsv462470CNV Loss19166990
    nsv327707CNV Loss16902084
    dgv6351n71CNV Loss21882294
    nsv882990CNV Loss21882294
    dgv6352n71CNV Loss21882294
    nsv518799CNV Loss19592680
    dgv6353n71CNV Loss21882294

    SABiosciences Cancer Mutation PCR Assays
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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section
    OMIM gene information: 606290    OMIM disorders: --

    2 diseases for PCDHGA3:    About MalaCards
    neuronitis    


    PCDHGA3 for disorders           About GeneDecksing

    Genetic Association Database (GAD): PCDHGA3
    Human Genome Epidemiology (HuGE) Navigator: PCDHGA3 (1 document)

    Export disorders for PCDHGA3 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
    About This Section

    PubMed articles for PCDHGA3 gene integrated from 9 sources:
    (articles sorted by number of sources associating them with PCDHGA3)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. A striking organization of a large family of human neural cadherin- like cell adhesion genes. (PubMed id 10380929)1, 2, 3 Wu Q. and Maniatis T. (1999)
    2. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PubMed id 20379614)1, 4 Rose J.E....Uhl G.R. (2010)
    3. The DNA sequence and comparative analysis of human chromosome 5. (PubMed id 15372022)2 Schmutz J.... Rubin E.M. (2004)
    4. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (2002)
    5. Comparative DNA sequence analysis of mouse and human protocadherin gene clusters. (PubMed id 11230163)1 Wu Q.... Maniatis T. (2001)
    6. Phylogenetic analysis of the cadherin superfamily allows identification of six major subfamilies besides several solitary members. (PubMed id 10835267)1 Nollet F....van Roy F. (2000)
    7. Large exons encoding multiple ectodomains are a characteristic feature of protocadherin genes. (PubMed id 10716726)1 Wu Q. and Maniatis T. (2000)
    8. Cadherin superfamily genes: functions, genomic organization, and neurologic diversity. (PubMed id 10817752)1 Yagi T. and Takeichi M. (2000)

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     ANDOR
    Aliases
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 56112 HGNC: 8701 AceView: PCDHGC3 Ensembl:ENSG00000254245 euGenes: HUgn56112
    ECgene: PCDHGA3 H-InvDB: PCDHGA3

    (According to HUGE)
    About This Section
      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for PCDHGA3 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    Patent Information for PCDHGA3 gene:
    Search GeneIP for patents involving PCDHGA3

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0 and Sirion Biotech, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Sirion Biotech, Cell lines from GenScript, and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or Enzo Life Sciences, In Situ Hybridization Assays from
    Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
    About This Section

     
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    GeneCards Homepage - Last full update: 23 Oct 2013 - Incrementals: 4 Nov 2013 , 7 Nov 2013 , 23 Jan 2014

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